Not what it seems
by Little Miss Sci-Fi
Summary: It's not all it seem in sam life. pleas read and review.
1. Chapter 1

Cassie stood looking at Sam standing in her very ugly wedding dress (in Cass opinion) she couldn't believe Sam was going to go through with this, a knock on the door of the room Sam was using to change, brought Cass back to reality one of the bridesmaids, one of Pete's family, opened the door and Jacob stepped in.

"Hey kiddo" he said as he hugged her, before turning to the others bridesmaids. "Can I speak to Sam alone for a moment," and they all went to leave.

Once they were out side Cassie went in search of one of her 'uncles'.

She found them outside; Jack and Daniel were arguing about something as usual and Teal'c…well Teal'c was just standing there when she approached she could hear their conversation

"Jack you can't just leave!"

"I'm not just leaving something came up at the base and I have to go back, Daniel," Jack said calmly

Daniel hushed his voice but Cassie could still hear, "You and I both know there's nothing wrong, and she'll find that out when she comes back in two weeks."

"Who says I'll still be here in two weeks Danny," Jack retorted

Daniel just stood there stunned Cassie took this moment to make her presents known "your leaving the SGC?" both men turned to face Cassie and Jack answered;

"Yes Cass, I'm going rather than-"

"Leave Colorado, without going to say goodbye to Sam" Cass finished.

Jack just looked at her, she could see in his eyes that this was the only way he could live if Sam married Pete. She nodded "ok" she whispered and stepped into his embrace.

"Have you talked to granpa George?" she asked

"Yeah he's thinking about it for now, and that I had the next couple of day's off due to this," Jack gestured to the church, "So I'm going to go up to the cabin"

Jack stepped back from Cass and kissed her on the top of the head.

"Come and visit me, huh?" she just nodded "You three better get moving or you be late."

The four said their goodbyes and Teal'c, Daniel and Cassie went back to the church.

From the door of the church Jacob and Gen. Hammond stood watching the goings on, and then Jacks dispatcher

"He gave me his resignation," George finally said.

"Did you except it?" Jacob asked

"I said I'd think about it," George answered

"What about the other thing?" Jacob asked

"I don't know, they haven't decided yet," he answered.

Jacob nodded and moved way from the door as the trio approached.

Cassie knew what she had to do, she was going to do it no matter what, and it was her duty to do it. The only thing is she didn't have a chance to before she was shoved into line with the other bridesmaids, she cursed to herself. Then it dawned on her and suddenly, she knew what to do.

Once Sam was standing on the alter and the priest began to speak;

Cassie was waiting to hear the part where her plan came into action

_If any of you can show just cause why they may not lawfully be married, speak now; or else forever hold your peace._

And that was it Cassie stepped forward said "I object" with everyone in the room looking at her, she never lost her nerve she had a job to do.

Sam looked at her "Cass what are you doing?" she asked.

"What I know is right! You shouldn't marry him" she thumbed in the direction of Pete

"And why the hell not?" he asked

"Well there are a number of reasons-"

"And they might be?" he asked

"Well if you let me finish my bloody sentence you ass hole I'd tell you" she spat angrily

"Watch it you or-"

"Or what you'll hit me"

"Cassandra Fraser!" Sam yelled, Cassie was taken aback Sam had never yelled at her like that, no one had. Once she had regained she looked into Sam's eyes and spoke whit hatred in her voice;

"Do what you think is best, but don't expect me to stand buy and watch you marry that ass hole, or while you destroy the life's of the people that **_love_** you and would **_die_** for you"  
with that she dropped the flowers in her hand's and walked out of the church.


	2. Chapter 2

"Do what you think is best, but don't expect me to stand buy and watch you marry that ass hole, or while you destroy the life's of the people that **_love_** you and would **_die_** for you" with that she dropped the flowers in her hand's and walked out of the church.

After Cassie stormed out of the church every one in the church started to talk and Sam turned to look at Pete, Jacob stepped up to Sam's side. "Sammy" he whispered she didn't answer she just looked into Pete's eyes, what she saw was pure anger.

She took a step back into her father, Pete tried to move towards her but Jacob had seen the look in his eyes as well, had seen the same look in Jones Harrison's before he had tried to hit Sam. He stepped forward and moved Sam behind him.

"Don't even think about it," he said through gritted teeth.

By now Hammond had also stepped up along with two SG teams. – Daniel and Teal'c had gone after Cassie – Pete apparently didn't now better than to mess with a bunch of airmen trained to kill, because he continued to move towards Sam.

Hammond moved his arm around Sam's waste and whispered "come on Sam lets get you back to the base" she didn't say any thing but she did move to leave Pete made a move to grab her, the SG teams grabbed him. Jacob and Hammond got Sam out of the church as quick as possible.

When the trio arrived at the SGC they went straight to Sam's on base quarters so she could change, while she was in the bathroom changing George and Jacob sat down and waited, when she emerged she was wearing a pair of baggy pjs. She stood in the door for a moment before speaking; it was a whisper that they barely heard, "I'm sorry."

Jacob stood and wrapped sam in his arms and let her cry, he carefully moved back to the bed where he had been seated, she cried for a while before she fell asleep. He laid her down on the bed and placed a blanket over her, he placed a kiss on the top of her head as did George before the two left the room.

Once the door was shut behind Hammond, Jacob turned to him, "Did you know?"

"Of course not Jacob, do you really think I would have let that happen to her again?"

George said slightly hurt that he would think that he would let that happen, "I was there the first time as well you now, I saw what it did to her."

Jacob nodded "I know I'm sorry" he said as Col Dixon and Major Frettie appeared around the corner both saluting the Generals.

"Sir's we took Mr. Shanahan into custody, and your son is on the surface wishing to speak to you sir," Dixon told Jacob.

"Keep Shanahan in a holding cell" Hammond said, as Jacob made his way to the elevator.

Once all four were in the elevator Jacob finally spoke.

"Where did Jack go?" he looked from Dixon to Frettie.

"Minnesota" Frettie answered, Jacob just nodded when the elevator doors opened they all stepped out

"I'll go see Mark" Jacob said making his way to the checkpoint

"Ok, Col Major thank you for informing me, you're both dismissed."

They both saluted their CO and moved off while Hammond made his way to his office to make a very important phone call.


	3. Chapter 3

"Minnesota" Frettie answered, Jacob just nodded when the elevator doors opened they all stepped out

"I'll go see Mark" Jacob said making his way to the checkpoint

"Ok, Colonel, Major thank you for informing me, you're dismissed."

They both saluted their CO and moved off while Hammond made his way to his office to make a very important phone call.

Jack parked his truck and walked towards the cabin, when his phone began to ring he was positive that it was the SGC ringing, he chose to ignore it.

Jacob reached the surface and nodded to the SF who moved away from his standing position next to his son, once the two were alone Mark spoke

"Where's Sam and why the HELL did the **_air-force_** arrest Pete?"

Jacob had rarely lost his emotions now, Mark was the reason Sam was in this mess, he set her up with Shanahan, he encouraged the wedding. And Mark also never knew what happened the first time some thing like this happened to Sam.

Jacob stepped forward and took hold of his son's arm; he took him to the elevators. Not answering any of Mark's questions. Once they reached a checkpoint he turned to Mark "Sign this, it basically says that any thing you see or hear on this base is confidential and you will be imprisoned if you speak of it to anyone."

Mark hesitated before signing, once he had Jacob turned and walked over to another elevator Mark just followed they went right down to level 27, neither spoke.

George was sitting at his desk on the phone to the president when there was a knock at the door and Jacob stuck his head in, George waved his friend in. He had a feeling Mark would be with him, he knew also that Mark was bound to say something to piss Jacob off.

"Yes sir they both just stepped into my office….yes sir," he put the phone on speaker, "They can hear you sir."

"Good. Jake it's been a while, how've you been?"

"Hey Henry I was hoping it was you, I'm fine a little pissed off but fine. You?" Jacob asked.

"I'm fine, so Mark are you there?" Henry asked

"Yes Mr. President" Mark answered

"Good Jake what did you tell him?"

Before he could answer Mark butted in, "Sir no offence but what's so special about a mountain, and all I wonted to know was why my sister just threw her life away and one of my friends just got arrested with out any good reason!"

Mark was yelling by the end of this.

"George" was all Henry had to say, the next thing Mark new he was sitting in the other office.

"What the HELL is going on" Mark yelled.

Jack hared a car pull up out side, then a door open and close, and a voice that he could never confuse

"Uncle Jack you around?" Cassie shouted as he open the front door

"Yeas kiddo what you doing here? Thought you'd be with Carter" he answered taking he into a hug

"I couldn't stand there and watch her marry him," she answered, "Not after what I found out," she mumbled.

Jack stared at her.

"What do you mean?"

Her head shot up to look at him, she never could really lie to him "I found out he was hitting her."


	4. Chapter 4

"I couldn't stand there and watch her marry him." She answered. "Not after what I found out." She mumbled.

Jack stared at her.

"What do you mean?"

Her head shot up to look at him, she never could really lie to him. "I found out he was hitting her."

Mark sat stunned for a long moment, before the anger appeared.

Before Mark could get a word in though, Hays spoke. "Don't even think about saying it, this may seem like a trick but its not. And you're very lucky that I agreed to give you clearance, now I have a lot to explain so shut up and listen like a good boy."

Hays explained most of the working of the SGC, Sam's work, their allies and enemies.

Once they were finished there was only one question on Mark's mind.

"So why tell me?"

None of them were expecting him to ask that, silence filled the room for a few minutes as they tried to find the best way to make him understand. Jacob recovered first.

"Mark there's something that we have to tell you that you may not want to hear or believe."

"You just told me you're an alien and you live on another planet." Mark retorted.

"True." Jacob paused before speaking. "You asked me earlier why we arrested Shanahan…" Mark nodded. "…the look in Pete's eyes reminded me of… something I'd seen before when it came to Sam."

"Love?" Mark asked.

"No actually, fury, the look that says 'I'm gonna hurt you so bad later.'" Jacob answered his son.

Mark took a moment thinking before he asked. "How do you know it was that? You… you could be wrong."

"Trust me Mark, I'm not. I know that look. It's the same look I saw in Jonas' eyes when George and I went to see her unexpected and found her laying unconscious on the floor. Trust me I know." He was angry at the fact that someone had done this to his little girl, again.

Jacob bowed his head and when he spoke next it was Selmac. "_I am sorry, Jacob is not able to speak at the moment, he is greatly worried and angry at all that has occurred within the last number of hours._"

Mark looked in shock at his father. Hammond spoke up. "Hello Selmac it's good to speak to you again." He then looked at Mark. "Mark this is Selmac the Tok'ra who shares Jacobs' body."

"_It is an honor to finally be able to speak with you Mark." _Selmac greeted.

Mark nodded, too shocked to do anything but stare at his father. Only, he realized it wasn't his father anymore. Knowing looks passed around the room as everyone gave him time to comprehend what he'd been told, filling him in and answering all the basic questions people ask went they met a Tok'ra for the first time.

Jacob calmed down enough to return and they finished filling Mark in on all the things he 'needed to know'. They said their goodbyes' to Hays and returned to the SGC.

They sat in silence in the briefing room for what seemed like hours each lost in their own thoughts before Dr. Lam walked in. "Sorry to interrupt Sirs, but you asked me to check Col Carter's recent medicals…"

"Yes, of course doctor please sit." Hammond indicated the seat next to Jacob.

"Well Sir, when I checked there were a few things that should've been looked into further, in my opinion. For example, there were several mysterious bruises that she claimed either occurred off world or in her lab from clumsiness. The worst I can find is an incident a few months back where she had two cracked ribs. She never came to me but Dr. Warner did examine her. She told him she had fallen down the stairs at home." Lam finished and looked at the three men around the table before speaking again. "I went to see her before I came up here, she seemed to be fine physically, but I gave her a sedative to help her sleep through the night."

Hammond nodded. "Thank you doctor, dismiss." She rose and left the room.

As soon as she was out Mark spoke. "I wanna see Pete." It wasn't a request it was a demand as he barely contained his rage.

Hammond and Jacob looked at each other before Hammond nodded, rising from his seat


	5. Chapter 5

As soon as she was out Mark spoke. "I wanna see Pete." It wasn't a  
request it was a demand as he barely contained his rage.

Hammond and Jacob looked at each other before Hammond nodded, rising from  
his seat

It was the early hours of the morning, he was now sitting on a plane on it's way back to the Springs with Cassie asleep next to him.

He had hopped the first plane back after he looked at his phone. There was a message from Dixon and Ferretti telling him to get his ass back ASAP.

He looked out the window, as the pilot came over the intercom announcing they would be landing in a few minutes. He turned to wake Cass only to see her looking at him.

"You ok kid?"

She nodded. "You?"

He nodded not trusting his voice.

As they filed off the plane Jack spotted Ferretti and Dixon coming their way.

"Hi Jack." Dixon said. Words unnecessary Ferretti and Jack simply nodded at each other.

The four piled into the SUV and headed to the SGC.

Hammond, Jacob and Mark stopped out side the brig door while the guard swiped his card to open the door.

"Can I speak to him alone first?" Mark asked.

Hammond and Jacob shared a look before Hammond finally agreed.

Mark walked into the room, when Pete saw him he jumped to his feet and walked over to the bars. "Mark, man am I glad to see you. What's going on? They won't tell me why I'm in here…"

Mark held up his hand up to silence him. "Don't Pete." He paused to control his  
anger. "I need to know… and I want the truth…did you hit Sam?"

"No I didn't Mark. How could you think that? If anyone did, it would've been O'Neill." Pete answered. "He probably ordered her to tell everyone I did it."

Mark nodded, turned to leave before turning back. "I set you two up. I thought you'd be good for her. You stand there and accuse one of the people that she thinks of as family…someone who would die for her… you're a worthless pig. I never won't to see again." Turning is back to him and left the room.

When Jack and the other's arrived he turned to Dixon. "Will you take Cass to the mess and get her some food then to see Hammond?"

"Where are you going?" Ferretti asked.

Jack didn't answer just left, hopping into another elevator and disappearing. The Colonel  
and Major looked at each other then back to where Jack had just been. Cass just shook her head and grabbed each man's arm. "He went to see Sam. Duh." She explained the obvious and dragged them towards the mess.

Jack made his way to Sam's room. When he got there Dr. Lam was just walking out. "General, your back."

"Since when do you call me General, Carol?" Jack asked.

"Since I became a doctor under your command, Sir." She retorted.

Jack smiled at her. "How is she?" He indicated to the door.

Lam floundered. "As well as could be expected. You can go in if you want." Jack nodded and walked past her, but waited till she had left before knocking. When he didn't received a response he opened the door and poked his head in.

She was lying on her bed with her back to the door, tossing and turning in her sleep. When he realized she was having a nightmare he moved into the room closing the door behind him, and swiftly making his way to her bed.

She was whimpering, saying things that sounded like "I'm sorry" and "no don't".

Jack whispered her name, not wanting to startle her but when that didn't work he spoke louder. She shoot up frantically searching the room before focusing on Jack and launching herself into his arms, trembling. He spoke soothing words of comfort to her until she calmed and looked up at him. It took her a few minutes to speak, when she did it was a whisper.

"I'm sorry, so sorry for hurting you…"

"Carter…"

"No, I know I hurt you… and I hurt you even more by asking you to go to that stupid wedding. I never meant to hurt you. Cass was right, but I was so convinced that I could have a normal life that I couldn't see that he wasn't what I really wanted. No I needed for that to happen."

Jack sat quietly for a minute before speaking. "As long as you're happy, I'm happy."

"But you weren't, that's the point, and I was too naïve to realize that. And don't lie to me, I see that now." Jack had no way of answering her because he knew she was right. He just nodded, and she gave a half smile, before giving a big yawn.

"I think it's time you got some sleep." He started to raise from the bed but her hand stopped him.

"No! Stay, please." Jack hesitated for a millisecond before kicking off his shoes and getting under the covers with her. It didn't take long for either of them to fall asleep


	6. Chapter 6

"But you weren't, that's the point, and I was too naïve to realize that. And don't lie to me, I see that now." Jack had no way of answering her because he knew she was right. He just nodded, and she gave a half smile, before giving a big yawn.

"I think it's time you got some sleep." He started to raise from the bed but her hand stopped him.

"No! Stay, please." Jack hesitated for a millisecond before kicking off his shoes and getting under the covers with her. It didn't take long for either of them to fall asleep.

When Mark came out Hammond and Jacob were standing waiting for him. They knew it hadn't gone well by the look on his face. Hammond decided not to bring it up.

"Why don't we get some food and then I'll have an SF take you to your hotel. I'm sure Karen is wondering where you are."

"Yeah, I should call her." Mark agreed. The three men made their way back to Hammonds office. Once Mark had finished speaking with his wife the trio made their way to the mess. Not to surprised to see it dead at this hour, except for one corner table occupied by two men facing the door and one young woman sitting with her back to them.

The one of the men was talking and the other was smiling. Once Jacob, Hammond and Mark has gotten food the three went to join them. "Colonel, Major may we join you?" Hammond asked.

"Of course Sirs." Dixon answered as both men stood. Once everyone was seated Jacob noticed the young woman was Cassie.

"Well if you aren't a sight for sore eyes. We were wondering where you'd disappear to?"

"Hello to you to Grandpa Jake, Grandpa George." Cassie replied.

"So where did you go to after you're masterful exit?" Hammond chuckled.

Cassie sent a glare his way before answering. "To Minnesota to see my stubborn Uncle."

"So it didn't go to well?" Jacob cringed.

"Oh no, it went fine. We got back about two hours ago. 'Beavis and Butthead' picked us up from Peterson." She said poking her thumb at Dixon and Ferretti.

"Hi, respect your elders young lady." Ferretti pointed his fork at her. "True you are old, and I respect you for admitting it." She smiled sweetly at him… he just glared at her.

Jacob smiled. "You're spending too much time around Jack. Speaking of which you said 'we', is he here?"

Cass nodded. "He went to see Sam when we arrived…haven't seen him since."

Mark spoke for the first time. "And that was two hours ago?" Cass nodded. Mark looked at his father questioningly.

"Leave it Mark. He wouldn't do anything to hurt her." Jacob warned. Mark nodded his understanding.

When they finished eating Hammond asked Dixon and Ferretti to take Cass to one of the guest quarters while he and Jacob took Mark to the surface.


	7. Chapter 7

Jacob smiled. "You're spending too much time around Jack. Speaking of which you said 'we', is he here?"

Cass nodded. "He went to see Sam when we arrived…haven't seen him since."  
Mark spoke for the first time. "And that was two hours ago?" Cass nodded. Mark looked at his father questioningly.

"Leave it Mark. He wouldn't do anything to hurt her." Jacob warned. Mark nodded his understanding.

When they finished eating Hammond asked Dixon and Ferretti to take Cass to one of the guest quarters while he and Jacob took Mark to the surface.

It was noon before either stirred. Sam woke first, mind still foggy from whatever Dr. Lam had given her the night before. It took her a moment to get her bearings and realize who's arm was draped around her waist. His breathing was shallow and warm against the back of her neck as she lay facing the wall with him spooned behind her.

She savored the warmth and security of his embrace for a long time before he started  
to wake, pulling her close and burying his face in her hair before speaking.

"Sleep well?"

Turning in his arms she could see genuine concern showing in his face.

"The best night's sleep I've had in a long time." She confessed. He smiled, drawing her closer as she tucked her head under his chin and rested it on his chest. He held her secure but gentle, not wanting to hurt her.

They lay in each others arms for what felt like hours, simply enjoying the contentment they felt being together, until it was broken by a knock on her door. Jack rose to answer the door, opening it to several very pissed-off Generals.

Jacob and Hammond sat in the briefing room at 11:00 facing the other occupants of the table, who had arrived at 9:00 hours, looking very annoyed.

The SF finally arrived. "Sirs?"

"Send him in airman." Hammond instructed. The young man left and returned a moment later ushering Shanahan into the room. Shanahan surprised, stopped dead in his tracks and paled visibly, recognizing the other occupants of the room. Gathered around the table were Generals Hammond, Carter and Ryan plus the Joint Chefs of Staff, Generals Ford (USAF), O'Connell (USMC), Jennings (USA), and Admiral Louse. And none other then President Hayes.

The airman behind Shanahan shoved him none to gently in his back to get him moving again.

General Ford was the first to speak. "Detective Shanahan, I suppose you'd like to know why you're here, as well as what would bring us all here also." Pete didn't respond, simply stood at the end of the table, waiting.

General Jennings asked, curious. "Did you even think about the consequences of your actions toward Colonel Carter?" Again Pete said nothing, paling even more, if at all possible.

General O'Connell added. "Not to mention she has lots of friends in high places, if you know what I mean."

This got a response from Pete, which probably wasn't his best move. "And what stupid  
alien would want to help a whore like her?" He seemed to have got some courage  
back, which didn't last long.

President Hayes felt compelled to ask. "Detective you do realize Colonel Carter is a highly decorated member of this base. She's saved the lives of many of the people in this facility. And every time you speak ill of her, you're pissing more and more of them off. For instance, the two guards standing behind you." Pete looked back and right into the face of two VERY pissed-off SF.

Admiral Louse asked. "Just out of curiosity, what gave you the idea that Col. Carter was a 'whore' detective?"

The whole table was surprised at the Admiral's question, but waited to hear Shanahan's answer. "I'm glad you asked, Sam's a whore because she's been sleeping with O'Neill for quite a while now." He snarled angrily.

"And what proof do you have Detective?" Ford asked.

Pete just smiled. "She's carrying his bastard child."


	8. Chapter 8

Previously….

Admiral Louse asked. "Just out of curiosity, what gave you the idea that Col. Carter was a 'whore' detective?"

The whole table was surprised at the Admiral's question, but waited to hear Shanahan's answer. "I'm glad you asked, Sam's a whore because she's been sleeping with O'Neill for quite a while now." He snarled angrily.

"And what proof do you have Detective?" Ford asked.

Pete just smiled. "She's carrying his bastard child."

And Now……..

Jacob was the first one through the door barreling straight for Jack. He connecting soundly with his nose, sending him to land heavily on the floor with blood streamed between his fingers and wondering 'what the hell was going on'. Sam had already jumped out of bed, and seeing what her father fury had done, was at Jack's side to check on his injury.

"What'd you do that for?" Jack asked, still holding his nose. Jacob went for Jack again.

"DAD!" Sam moved in-between the two men, Jacob just barley stopped in time.

Jacob calmed, realizing what he'd done, began backing away to where the Joint Chefs, Hammond, Ryan and the President stood.

Sam stood glaring at Jacob with cold rage in her eyes. "Why the hell did you hit him?" She screamed. When Jacob didn't answer she looked at the rest of the men in the  
room. "WELL?"

Hayes spoke up. "Sam you know how your father is. What would you expect him to  
do if Jack answered the door to your quarters?" They were in a stare-off and one thought kept running through Jack's mind '…if looks could kill…'.

"Do you really expect me to believe that bull. Dad knew full well the General was here. Cass would have told him that last night."

"Well, if you'd heard what we'd heard this morning you'd understand." Jacob muttered.

"And that would be…?" Jack asked letting the 'what' go unsaid waiting, from his position slightly behind Sam, knowing they would never hit her, him, he wasn't so sure.

Jacobs' anger seemed to have returned. "That you got my baby girl pregnant!" Jacob again lunged for Jack. Sam placed herself squarely between the two men.

"And how the hell could he have done that? Because I sure as hell didn't sleep with him. Where in god's name did you get that idea?" Sam yelled not just at Jacob this time but the others behind him as well.

Hammond answered. "Detective Shanahan."

Sam was furious, and she was gonna let them know it. "And you believed him!" She  
yelled.

"Now wait one moment Colonel…" General Ford started to say.

"No I will not. You actually believed that sociopath I nearly married? What in god's name made any of you actually think we'd destroy both are careers and most likely land the General in Leavenworth!" She was screaming by the end, she was so confused and dizzy…and…all of a sudden the world went black.

Jack jumped forward to catch she before she hit the floor. He gently laid her on the floor and checked her pulse…there it was. He breathed a sigh of relief. Jacob was kneeling next to him as the others gathered around. One of them had called for a medic team. It seem forever before Dr. Lam arrived. She and her team went to work on Sam and after a few more minutes she ordered her team to take Sam to the infirmary, turning to the men standing in the room.

"What exactly happened?" She asked Jack.

"Carter was yelling then she collapsed. That's it." Jack answered. "She's ok right?"

"Yes Sir, she'll be fine. By the looks of it she hasn't eaten in a few days and she overtaxed herself using up the last of her energy yelling at you."

"Them." Jack said pointing to each of the others in the room returning his eyes to a very confused looking Dr. Lam. He explained. "She was yelling at them not me."

She nodded. "Sorry, I assumed you were being yelled at because of the nose." She pointed to the blood on his shirt and face.

"No, that was me." Jacob confessed.

Lam looked from him back to Jack and nodded. "I'll wanna have a look at that Sir…make sure it's not broken."

"It's not. Trust me… I'd know if it was." Jack said.

"Still I'll wanna have a look at it. " Jack just nodded knowing how stubborn this woman could be. "Besides, you'll be in the infirmary anyway seeing Colonel Carter…so shall we Sirs." She indicated with her hand, Jack nodded falling into the head of the line following her down the hall.

When they reached the infirmary Dr. Lam checked Jack's nose and confirmed it wasn't broken. He was seated on the bed next to Sam while the other men stood around Sam's bed. When Dr. Lam finished checking Jack she turned to see her other patient.

General O'Connell stepped up to the end of Sam's bed. "Doctor would you be able to  
answer a question for us?" She looked up from the chart she'd been studying and nodded. "Have you seen anything in the Colonel's medical records that says she might be pregnant?" Jack didn't say anything knowing that this was the only way they would believe them.

Lam looked at Jack in confusion so he explained. "Shanahan told them that Carter and I have been having an affair, and that Carter was pregnant with my kid." She just looked at the men in the room and back to O'Connell. Normally she would never discuss a patients medical records with anyone other than her Commanding Officers, but in this case there really was nothing to discuss.

"I don't believe so Sir. If you wish I will run a pregnancy test on her. But, if I may speak freely…" He nodded. "…I sincerely doubt she is. Neither Sam nor Jack or dumb enough to screw up there careers'. And, even if they were, why would Sam agree to marry Mr. Shanahan?" With that said she moved away from Sam. "I'll run that test now Sir."


	9. Chapter 9

Previously………..

Lam looked at Jack in confusion so he explained. "Shanahan told them that Carter and I have been having an affair, and that Carter was pregnant with my kid." She just looked at the men in the room and back to O'Connell. Normally she would never discuss a patients medical records with anyone other than her Commanding Officers, but in this case there really was nothing to discuss.

"I don't believe so Sir. If you wish I will run a pregnancy test on her. But, if I may speak freely…" He nodded. "…I sincerely doubt she is. Neither Sam nor Jack or dumb enough to screw up there careers'. And, even if they were, why would Sam agree to marry Mr. Shanahan?" With that said she moved away from Sam. "I'll run that test now Sir."

And Now……..

After Lam left, Hayes turned to Jack. "We need to speak to you in private, General." Jack looked up from staring at the floor.

"Yippy, …getting accused of something else I didn't do too." He mumbled as he hopped off the bed. "Can I at least, shower and change before I'm accused of something else Jake will most likely want to punch my lights out for?" Hayes nodded and told him to meet them in the briefing room when he'd finished.

Jack showered, shaved and dressed in his usual green BDU. Upon reaching the briefing room Jack could see his superiors and Jacob talking. When he walked in the room fell silent. He stood by the door until General O'Connell spoke up.

"Come in and shut the door General." Jack did as told. "…and sit down." Again he  
did as he was told.

Jacob sat across from Jack, he looked into the younger man's eyes, before lowering his own, his eyes flashed and Selmac spoke. "I wish to apologies for not stopping Jacob earlier. I was unable to, even though I believe you would not jeopardize Samantha's career. It is my belief that if you were going to act in that manner, you would have done so many years ago, and Samantha would never have met Detective Shanahan. Once again, I am sorry."

"No prob', I'm not actually that surprised he hit me. I'm more surprised that he and the rest of them believed Shanahan without even hearing our side first." Jack said.

Selmac bowed his head again, this time Jacob spoke. "Yeah well. we'll believe you once the test comes back."

"You have that little faith in your own daughter?" Jack was outraged. "She bust her ass to make you proud of her. She's a damn fine soldier and the most brilliant person on this planet. She has the love and respect of everyone on the base, with the exception of the men in this room, it would seem. All it takes is some jerk off the street making a stupid accusation and you all doubt her. I know…I know." He through up his hands. "Things have to be checked out. But you, Jacob, you should know Sam better. George?" Jack was furious, pacing from one end of the room to the other, arms waving in the air like he might take flight any minute. He finally ran out of stream and faced off, focusing on Jacob and Hammond. "How could you treat her like this?" Before collapsing into a chair at the far end of the table. It was a more passionate plea then anyone had ever heard Jack make. The room fell to total silence as everyone took stock.

At that moment the door opened and Dr Lam entered followed by Sam.

Soon after everyone left the infirmary Sam woke. Dr. Lam noticed and walked over to her.

"Well good morning Colonel. How are you feeling?"

"Fine now, thanks. How long was I out?"

"About an hour and half. We gave you fluids, and I was ordered to run a test on you."

"A pregnancy test?" Sam cut in.

"Yes, the Joint Chefs ordered it. I have the results now. I'm glad you're awake. I really wasn't comfortable during this without you consent or knowledge." She ran out still studying Sam's face.

"They have every right." Sam acknowledged. "They're my superiors and the accusation has been made. Like it or not, they have to investigate. It's the way the system works." Sam seem to be taking it all in stride. Ever the 'good soldier'. "Pete's another story entirely." She let the threat hang.

"Would you like to know the results?" Carolyn asked glad to be relieved of the burden of going against her patient's wishes.

"I'm sure I already know the answer, but yes, please." Sam responded with confidence.

"The test came back negative. I ran it twice to make sure." Sam breathed a sigh of relief. She was pretty sure Pete hadn't gotten her pregnant, they didn't have much of a physical relationship anymore. Hard to get in the mood when you're being beaten. But now everyone would believe her and see Pete for what he really was. She wasn't sure how she would've handle carrying Pete's child. Now she wouldn't have to find out.

"I was just about to go see them. I think General O'Neill will be there as well." Carolyn said, pulling Sam out of her musings. "Would you like to come along? I don't see any reason to keep you here, as long as you go get something to eat after we're finished." That suited Sam, she dressed quickly and the two made their way to the briefing room.

When they entered and sat General Ryan got straight down to business asking if the test results came back. Lam gave her results to a very subdued audience. No one seemed to be able to make eye contact with either Sam or Jack. They both seemed to be taking it all in stride and accepted it as the price of doing business as the military. The tension evaporated and they fell back into a normal friendly mode, discussing ways and means of handling Pete and the trouble he had caused. Lam excused herself saying she had patents to see, her part complete.

Once they were finished talking Hammond suggested getting some food, which  
they all agreed on.


	10. Chapter 10

Previously…….

When they entered and sat General Ryan got straight down to business asking if the test results came back. Lam gave her results to a very subdued audience. No one seemed to be able to make eye contact with either Sam or Jack. They both seemed to be taking it all in stride and accepted it as the price of doing business as the military. The tension evaporated and they fell back into a normal friendly mode, discussing ways and means of handling Pete and the trouble he had caused. Lam excused herself saying she had patents to see, her part complete.

Once they were finished talking Hammond suggested getting some food, which  
they all agreed on.

And Now…………

After eating and chatting for a while Sam went off to her quarters on base for some much needed rest. The others returned to the briefing room to discuss Jack and Sam's future. Jack headed off to handle some unfinished business.

"So what are we going to do about this, because we all know they aren't going to go back to the way things were before?" Jacob was the first to pose the question as soon as everyone was seated.

"Yes, but resigning isn't an option either…for either one of them. They're both too valuable to the program to just let them go. The SGC needs them, the country needs them. They're both irreplaceable, they bring a uniqueness we can't get from anyone else. Colonel Carter knows more about the StarGate than anyone else on the planet. And General O'Neill…well, he may play dumb…but he's what keeps this program going We can't afford to loose either one of them." Admiral Louise pointed out.

"What about moving Colonel Carter into a civilian position? She could still be in charge of the labs and even join in on field missions occasionally." Jennings asked.

"No, that would mean breaking up SG-1. Jack would never want her give up her career. She's worked too hard getting where she is, to just walk away from it now." Hammond explained.

They all agreed as silence descended, all trying to think of an option everyone could live with. "What about Jack resigning his commission?" Jacob asked at long last.

"Jacob, we just said that we can't afford to lose him. The Asgard love him and so do most of our other alien allies." Pointed out General Ryan.

"No, I mean allow let him to resign from the Air Force, but leave him to run the base as a civilian. It's been done before and everyone already respects him, military and civilians alike. Beside it would look better having the base under civilian control if or when the StarGate program does goes public.

"You have a point, but will he agree to it? Jack loves the Air Force." Hayes questioned.

"Not as much as he loves Sam." Jacob quietly assured everyone, even through he could see the unease on the faces of the Joint Chiefs as voice was given to what they had all known for sometime.

"I don't know about this. There would still need to be rules and regulations governing relationships and behavior even between civilians and military personnel. O'Connell added.

"Yes, but come on Jack's a soldier, has been all his life. He knows better than to allow his feeling to get in the way of him doing his job. Hell, he's proved it repeatedly over the last eight years. Or have you all forgotten he shoot her twice with a zat…in the line of duty. I doubt anyone here could say for sure he'd be able to do the same if you'd been in his shoes." Jacob had run out of steam, returning to his seat he finished. "Come on, we just accused him of breaking the one rule that has kept them apart all these years. He'd leave us in a heart beat.

They all knew he was right. "Ok, we'll see what he has to say." Hayes finished up for everyone.

Jack stood in front of the door to the holding cell. Inside, the man he'd nearly let take away from him the one thing that meant more to him than anything else in the world.

Shanahan looked up to see who had walked in and smiled. "So, the man who took my fiancé away from me has finally decided to graced me with his presence."

"Did you really think that telling them I got her pregnant would work? You had to know they would give her a test and it would show you were lying." Jack said calmly.

"Not if I'd already gotten her pregnant. But, you won't be able to prove that it wasn't yours until long after your Court Marshal, General." Drawing out Jack's title mockingly as he continued to gloat.

"She's not pregnant at all Shanahan." Jack spelled it out for him slowly. "And especially not by scumbag like you." The calmer Jack remained the angrier Pete became.

"You're lying!" He yelled.

"Nope, Doc got the results about an hour ago, she's not pregnant."

Pete looked angry and ready to kill as his thoughts turned inward. After only a few seconds an evil smile split his face as he twisted the knife trying to hurt Jack more. "Oh well, I still got what I wanted. I still got to fuck her brains out while you sat in your lonely house. God, she was a great fuck, especially when she fought back. Great little fighter she was too, but I could always make her stop fighting by telling her I'd kill you."

Jack was calm on the outside, inside all he wanted to do kill him with his bare hand. Squeeze the life out of him, slowly. To watch him die a slow and painful death for the things he had done to Sam. Through his fog of rage it finally registered what Pete had actually said. "You raped her?" Jack's voice was barely above a whisper and dangerously calm.

"Oh yes I did over and over again and there's nothing you can do about it. If you lay one hand on me I'll press charges. I know people who can make you disappear. You have no idea the amount of trouble I can cause you and your little pet whore if you so much as touch me." Pete taunted and dared.

Jack just smiled. "You really are an idiot, you know that." Jack pointed to the camera amounted from the ceiling in the far corner of the room. "You just admitted to raping and beating a USAF Colonel on camera and threatening to kill a USAF General." Turning to leave Jack turned back to face him. "I cant wait to see what you get for this Shanahan." Jack left Pete to stew and think about everything that had just happen. He was off to Sam's room to check on her. He realized now why she had wanted him to stay the night with her.

When he reached her room he could her noises coming from inside. He quietly opened the door to find her tossing and turning in a nightmare. He moved to her side, placing a hand on her shoulder and gently waking her.

"Sam, Sam wake up baby…it's okay…it's just a dream." You could see the disorientation and fear clearly on her face as she took in her surrounding. She eyes finally came to rest on Jack. She threw her arms around his neck and burying her in his chest and cried for what seemed like hours before she regained some control of her emotions.

"I'm sorry. I…"

"Don't be sorry, not to me please. Answer me one question. Why didn't you tell me last night he raped you?" Sam's head shot up and looked him in the eye for a split second before looking away in shame.

"Because I thought you'd think that since I couldn't stop him from…from….from raping me, that I just gave up trying. Or that I wanted him to do…that to me." She tried to move away from him but he held her close.

"I would never think that Sam. You are one of the strongest, smartest and most beautiful women I've ever met." He looking away when he spoke again, just barely above a whisper. "I know how hard it is to deal with being raped." He confessed to her.

Sam gently placed a hand on his cheek and made him look at her. What she saw in his beautiful brown eyes was understanding…understand born of a shared experience and the same fear she had. She had known he was held prisoner in Iraq. She had just never thought about what that would mean in his day to day life there. Now she thought she understood a little. She gently traced his cheek line with her thumb before he pulled her into his arms and buried his face in her hair.

They were interrupted some time later, still in each other's arms. Jack moved to open the door, joking…"I hope that's not Jake come by to actually break my nose this time. Trying to lighten the mood. It made Sam smile. His job was done.

Sam moved in front of him, opening the door to reveal Walter standing there waiting. "Sorry Ma'am, but you're wanted in the briefing room, as well as the General." Sam smiled again, sending him on, saying they'd be there in a minute. She closed the door and chuckled slightly.

"What?" Jack asked.

"I'll never understand how he seems to know everything including where to find you."


	11. Chapter 11

Previously…..

Sam moved in front of him, opening the door to reveal Walter standing there waiting. "Sorry Ma'am, but you're wanted in the briefing room, as well as the General." Sam smiled again, sending him on, saying they'd be there in a minute. She closed the door and chuckled slightly.

"What?" Jack asked.

"I'll never understand how he seems to know everything including where to find you."

And Now…………..

Jack and Sam hurried on to the briefing room, not wanting to keep so many high ranking officers waiting. They arrived to find everyone waiting around the table, Jacob with his back to them.

"Sirs', you wish to see us." Sam said, coming to a prefect military 'parade rest' stance and awaiting further orders. Even Jack pulled up short and gave the men before him their due as his superiors. Hayes waved away the formalities, indicating they should take a seat. Which they did, still tense awaiting a decision on both their futures.

"Yes we did. We've talked among ourselves. We decided we can't accept either of your resignation. But, we're also assuming neither of you is interested in returning to the way things were before. Are we correct in that assumption?"

With a shared look they said in unison… "No Sirs, we're not." Jack continued. "Sir, I'm more than willing to re-submit my resignation as head of StarGate Command. I'll resign effective immediately. Hayes was already prepared and cut him off before he could go any further. "Request denied General. You're too valuable, we need you here to run the SGC…and before you say anything, the same goes for you also Colonel.

Sam and Jack were confused. Jack's temper began to flare. "So, let me get this straight. You're not gonna accept our resignation. And you can't give us a waiver to pursue a relationship…so why even bother to ask us if we wanted to go back to the way things were if that's the only option you're giving us. 'Angry' was an understatement, Jack was beyond pissed and he didn't mind them seeing it.

Jacob finally spoke up, back still turned to them. "Which do you love more Jack…Sam or the Air Force? "

Before Jacob could finish the question Jack answered. "Sam." He answered as through it was a given. And for him it really was a given. There was nothing he wouldn't do for her. He finished for Jacob ear mostly. "That's a stupid question and you know it Jake. I would've retired the moment I met her, if I could've, hell I tried more than a few times over the years. He admitted.

Sam stared open mouth at him, in shock at his revelation. "You did?" She turned still in awe. Jack nodded in answer to all the unspoken questions he could see in her eyes.

Jake finally turned around. "Good, I was hoping you'd say that." As if that one answer explained all the mysteries of the universe.

"But what difference does it make if we still can't be together?" Jack asked already frustrated.

"Oh but you can." Jake teased him with a smirked on his face.

Jack stared from one man to the next as understanding dawn on him. "You'll allow me to retire from the Air Force and continue to command this base but as a civilian." He finally saw the light as he posed the question to President Hayes.

"Yes, if you'd be interested in the position." The President confirmed for him. "You already have the respect and loyalty of everyone here. Nothing would change in the way you run the base, only your title.

Jack turned to Sam to get her reaction to the proposal. "It's your decision." Sam conceded before he could ask the question.

Jack simplified his stances. "If I say no, there's no us…if I say yes…there is. You know how I feel Carter. How about you? How do you feel about all of this?" Jack needed to give Sam a chance to have some say in their future and not just presume to make decisions for her.

"You know full well what my answer will be." Understanding he was giving her an 'out' if she wanted one and loving him even more because of it. She loved Jack very much, but wasn't looking forward to saying so in front of the President, Joint Chiefs, General Hammond and her father, even though she was pretty sure they all already knew.

Jack sat thinking for all of a millisecond before answering. "I'll do it." Still trying to grasp what this would mean for his and Sam's future.

Two days later Jack went to work as the civilian commander of the SGC. Three month's after that Pete was put on trial for the rape and abuse of Sam. He lost. He was sentenced to 15-20 years for his crimes.

On 27th of January 2007 Jack was presented a beautiful baby girl. Laying one bed over in the infirmary was the most beautiful blonde he had ever seen in his life. She was exhausted and sleeping soundly. She had every right to be tired. Looking down in his arms he start a new set of blue eyes staring back at him. Smiling down at her and tickling his finger under her chin he greeted her from her nap. "Hello my little angel." When he looked back up he looked straight into another more familiar set of beautiful blue eyes. "And there's my other angle. Did I wake you?" Taking her hand.

"No, I was already awake." She answered. Jack leaned in and gently kissed her on the forehead. Brow furrow in confusion she ask. "What was that for?"

"For giving me a second chance. If anyone had told me a years ago that something like this could ever happen to me, I would've have laughed in their face. But you, Samantha Elizabeth Carter O'Neill have given me that chance, and you gave me a beautiful little girl as well. I thought your wedding with Pete was the worst thing that could ever happen to me. It turned out to be the best. I guess things are not always what they seem. Thanks you." He kissed her again. She smiled at him, not needing to say anything.

"So what have you decided to name for our little angle?" she teased.

Jack looked at her, "Grace Elizabeth Carter O'Neill, if that ok with you?" Sam smiled and nodded. "Happy anniversary." He leaned in and kissed her again.

The End !


End file.
